Patch concatgffs ick4

bin/repeatmasker_liftoff.py

@@ -61,6 +61,8 @@ def annotation_main():
 
     #gather ref sample id
     ref_id=ref_gff['seq_id'][0]
+    print(f'refgff is {args.refgff}')
+    print(ref_gff.head())
     #gather index of attributes for first and second ITRs; needed for repeatmasker ITR attributes
     first_ITR_index=ref_gff[ref_gff['attributes'].str.contains("ITR")].index[0]
     last_ITR_index=ref_gff[ref_gff['attributes'].str.contains("ITR")].index[-1]

modules/local/concat_gffs/main.nf

@@ -21,14 +21,10 @@ process CONCAT_GFFS {
 
 	input:
 	path ref_gff_path
-	//path repeatmasker_gff
-    //path liftoff_gff
-    tuple val(meta), path(repeatmasker_gff), path(liftoff_gff)
-	tuple val(meta), path(fasta_path), path(fastq_1), path(fastq_2)
+    tuple val(meta), path(fasta_path), path(fastq_1), path(fastq_2), path(repeatmasker_gff), path(liftoff_gff)
 
 	script:
 	"""
-    echo "repeatmasker_liftoff.py --repeatm_gff $repeatmasker_gff --liftoff_gff $liftoff_gff --refgff $ref_gff_path --fasta $fasta_path  --sample_name $meta.id"
 	repeatmasker_liftoff.py --repeatm_gff $repeatmasker_gff --liftoff_gff $liftoff_gff --refgff $ref_gff_path --fasta $fasta_path  --sample_name $meta.id
 	"""
 

subworkflows/local/repeatmasker_liftoff.nf

@@ -13,7 +13,7 @@ include { CONCAT_GFFS                                       } from "../../module
 workflow REPEATMASKER_LIFTOFF {
 
     take:
-        fasta
+        fasta // meta, fasta_path, fastq1, fastq2
 
     main:
         // run repeatmasker annotation on files
@@ -31,24 +31,23 @@ workflow REPEATMASKER_LIFTOFF {
         repeatmasker_gff_ch = REPEATMASKER.out.gff.collect().flatten()
                 .map { 
                     meta = [:] 
-                    meta['id'] = [id:it.getSimpleName()] 
+                    meta['id'] = it.getSimpleName()
                     [ meta, it ] 
                 }
 
         liftoff_gff_ch = LIFTOFF_CLI.out.gff.collect().flatten()
                 .map { 
                     meta = [:] 
-                    meta['id'] = [id:it.getSimpleName()] 
+                    meta['id'] = it.getSimpleName()
                     [ meta, it ] 
                 }
 
-        concat_gffs_ch = repeatmasker_gff_ch.join(liftoff_gff_ch) // meta.id, fasta, repeatmasker_gff, liftoff_gff
+        concat_gffs_ch = fasta.join(repeatmasker_gff_ch).join(liftoff_gff_ch) // meta.id, fasta, fastq1, fastq2, repeatmasker_gff, liftoff_gff
 
-        // concat gffs
+        // concat gffs 
         CONCAT_GFFS (
            params.ref_gff_path,
-           concat_gffs_ch,
-           fasta
+           concat_gffs_ch
         )
 
     emit:

subworkflows/local/submission.nf

@@ -36,7 +36,7 @@ workflow INITIAL_SUBMISSION {
             // drop fasta_path from ch
             submission_ch = submission_ch
                 .map { 
-                    it -> [it[0], it[1], it[3], it[4]] 
+                    meta, _, fq1, fq2 -> [meta, fq1, fq2]  
                 }
             SUBMISSION_SRA ( submission_ch, submission_config )
 
@@ -51,7 +51,8 @@ workflow INITIAL_SUBMISSION {
             // drop fastq paths
             submission_ch = submission_ch
                 .map { 
-                    meta, _, fq1, fq2 -> [meta, fq1, fq2] 
+                    it -> [it[0], it[1], it[2], it[5]] // meta, fasta, gff
+                    //meta, fasta, _, _, gff -> [meta, fasta, gff]  // duplicate underscore error
                 }
             SUBMISSION_GENBANK ( submission_ch, submission_config )
 

workflows/tostadas.nf

@@ -153,6 +153,9 @@ workflow TOSTADAS {
         GET_WAIT_TIME (
             METADATA_VALIDATION.out.tsv_Files.collect() 
         )
+
+        submission_ch.view()
+
         INITIAL_SUBMISSION (
             submission_ch,  // meta.id, fasta, fastq1, fastq2, gff
             params.submission_config,